A former pastor who waged a lengthy battle with the province in the 1980s over the licensing of his privately run school is back before the courts, this time to face charges in connection with the historical sex assault of two students.

Thomas Larry Jones, 69, who now lives in Carstairs, has been charged with indecent assault of a female, three counts of gross indecency, four counts of sexual assault, two counts of sexual interference and two counts of sexual exploitation.

Calgary police allege the abuse of one of the victims began in 1979, when the girl was five, and continued until she was 15. The abuse of a second girl began in 1986 when she was nine, and continued until she was 18, police said.

At the time, Jones was the pastor of the Western Baptist Church in the northwest community of Montgomery and also ran his own school, the Western Baptist Academy, out of the church basement.

Det. Jeff Klinger with the child-abuse unit said in both cases, the girls attended the church and were also students at the school, adding the assaults allegedly took place at the church and at the accused man’s home next door.

Klinger said one of the victims first came forward to police in 1993, but there wasn’t enough evidence to proceed with an investigation.

But after Russell Louis Rodman, another leader at the same church, was charged in 2012 and convicted in 2013 of sexually assaulting four boys in the 1980s and 1990s, police were able to reopen the Jones case.

“During that (Rodman) investigation, officers spoke to a number of people involved in the church at the time, including a number of youth,” Klinger said. “During those interviews, a disclosure about Mr. Jones was received.”

He said there was no indication that Rodman and Jones were “working together in any way,” adding it’s rare for two spiritual leaders from the same church to be facing sex assault charges in connection with different victims.

Officers were challenged with tracking down people to interview, due to the passing of decades, name changes and new homes out of Calgary, Klinger said.

Once police had gathered enough evidence, they notified Jones, who turned himself in to Calgary police on Wednesday and was subsequently charged.

Pastor Michael Martin, the current leader of the Western Baptist Church, said he and other members of the church were “shocked” to learn of the charges.

Martin said he is friends with Jones — who goes by his middle name, Larry — and calls him a “very caring man.”

“These are allegations,” Martin said. “We’ll just wait and see what happens.”

He said Jones left the church sometime in the 1990s and moved to Carstairs, where he was leading a semi-retired life.

He was no longer a church leader at the time of his arrest, police said.

In the 1980s, Jones was locked in a years-long dispute with the province for refusing to obtain a provincial licence for his school, a battle that included a trip to the Supreme Court of Canada. He was also fined for keeping his children — who attended the academy — out of a certified school.

In an interview with the Herald in September 1987, Jones said he believed that God had instructed him to teach his children, that the province had no business butting in and that he was prepared to face jail time over the dispute.

“God is on our side,” he said at the time.

Eventually, just before the province was set to take Jones back to court, he signed an agreement with the department of education, which allowed the school to continue operating without a licence as long as it could supply information about students, teacher qualifications, tests and curriculum.

The school is no longer in operation, Martin said.

Jones was also charged in December 1989 with a number of firearms-related offences and with uttering threats after a confrontation with a youth at his home, but those charges were later stayed.

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